Knuspr

Main Reference

Gruene, T and Sheldrick, G M
Geometric properties of nucleic acids with potential for autobuilding Acta Crystallogr. 2010, A67, 1-8
BibTeX file doi:10.1107/S0108767310039140

License Information

The source of Knuspr and its GUI are licensed under a Creative Commons Attribution 3.0 Unported License. By agreeing to the license, you agree that "appropriate credit" means citing the above publication.

Binaries and Source Code

Knuspr ("Kinderleichtes Nukleinsäure SuchPRogramm") was my main research topic between 2004 and about 2011. The program finds the positions of phosphates and bases in electron density maps with a fairly high degree of reliability. knuspr is particularly useful in combination with RCrane. In order to make both programs work together you should install the GUI knuspr-gui.

The user name to access these files is knuspr, the password is "oshaeM6IeM". I hope this prevents robots from downloading the source without agreement to my license.

List of files for the knuspr program

OS	Platform	File	md5 message digest
source	n/a	knuspr-2016-07-13.zip	58914b75cabcdd7e1b2e97d2ed7fb9f6
Linux	64bit	knuspr64bit_linux-2013-08-12	86e80eda68be409fd23483d838b32373
Linux	32bit	knuspr32bit_linux-2013-08-12	a9c6d8ae4815c4119eaa826cefe54e5c
Linux	64bit	knuspr64bit_linux-2016-07-13 (dynamically linked)	89786fc3c5d54d685e5b6c9fac70bd91

Beware that the Linux binary of the latest version 2016-07-13 is dynamically linked: you will need the runtime libraries from ccp4c, clipper, gsl, gomp, and fftw in addition to more standard libraries. It has become cumbersome to link statically against clipper and ccp4c, and these to libraries have become available in the standard repositories in many distributions, hence there is little need for a statically linked version.

If you do need the statically linked version, it is most likely safe to use the 2013-08-12 version: the single bug fix in 2016-07-13 has been reported to me a only once!

knuspr GUI: Combining knuspr with RCrane

Moritz Wette has developped a graphical user interface that allows using knuspr from within coot. It also acts as an interface to RCrane, i.e., to GUI passes the output from knuspr on to RCrane. The package you need to download for using knuspr-gui contains a README.txt with installation instructions. Note that you need access to your coot installation.

This code was successfully tested with coot 0.8.2-pre (revision 5502) and python 2.7.8.

List of files for the knuspr GUI

OS	Platform	File	md5 message digest
Mac OSX and Linux	n/a	knuspr-gui_2015-02-20.tar.gz	76dc452d1c850cb911f38b61f0de2942

Moritz Wette's work was supported by the DFG grant GR 4216/1-1.

Tim Gruene

Last modified: Mar 25, 2020 22:41